Sho me the money
The big difference with a TSO panel mount IFR GPS (besides money) is the TSO, it must meet those specs (by test and documentation) a handheld does not. It is not reliability. I can't quote you the exact specs but the IFR GPS has more fault protection and annunciations. Also the software is written to work so it conforms to the TSO, which the handhelds are not held against. This is the reason for the cost, they spend more time and money flight testing and documenting them. This gives the handheld some flexibility in design and gee-wiz graphics. Plus a portable really does not need to meet any Regs. We (experimental) can mount our portables GPS in the panel. This is a NO NO in a factory plane. Yes it is a reg, but if you fly IFR and are off laterally just a little on an approach by entering the wrong waypoint or missing that the GPS has lost accuracy, it could kill you. Thus the tighter (restricted) operating functions (approach mode) and how waypoints cycle.
Mo money mo money. With a handheld GPS you get more features and a larger screen for half the money. Also most handhelds can be coupled to autopilots. You can take it with you, home, hotel or FBO to flight plan. The new portable GPS have terrain warnings that most panel mounted GPS don't have at this time, except a few high-end units. Also many of the portable GPS can work in your car as well.
Panel mount will cost more, do less and have small (mono-chrome) screens.
Panel mount IFR GPS: Yes they have large screen color panel mounted GPS's that will show weather, (TCAS) other aircraft traffic, inst approaches and have integrated Nav and com radios. We are talking mega bucks. The full meal deal panel mount GPS with Com radio and Nav radios, VOR/LOC/GS receiver, cost over $8-$12 grand and more. Add weather and traffic (transponder) is more money than I would think of spending on a small sport plane. Even than the screens are small or limited in color. To get terrain you need another $7.5 grand for a MX20.
Panel mount VFR GPS/COM: VFR panel mount GPS's that combine a COM radio with the GPS are nice, but you are going to pay for it and still have a small screen. Apollo/Garmin has some nice ones but some models are out of production. You can buy a new handheld GPS ($1000) with huge color screen and a separate panel COM ($600-$900).
EFIS/GPS combo: EFIS with GPS map display such as Blue Mountain or Grand Rapids Technology is a great combination, GPS integrated with flight attitude and flight instruments. A nice option but more money. A Dynon EFIS (no gps Nav) is about $2K and with a handheld GPS it would be about $3K. Prices of the EFIS with GPS are coming down to that $3K mark. EFIS/GPS lite may be a good option if you are going EFIS, instead of a handheld GPS and separate EFIS. You loose a little flexibility (like take the handheld GPS take it with you/use in car/boat/plane) but a nice integration of components. Can you do IFR approaches with these systems? Subject to debate.
Unless you are going IFR a hand-held is the hands-down winner in the bang for bucks department. Handhelds have bigger screens and much cheaper.
A handheld GPS can be bought for $300 (used) to $1,500 for the latest new gps.
Here are some suggestions (no particular order)
Garmin 296 (used $1350, new $1500, latest w/ terrain obstacle warnings)
Garmin 195 (B&W but very powerful out of production ($300-$400)
AvMap EKP-IV,
http://www.avmapnavigation.com/ ($1400 huge screen)
Lawrance 1000c (about $1000 very large screen)
Lawrance 1000 (large screen B&W bargain priced, very nice)
PDA based system and software:
http://anywheremap.com/ (standard in PDA software)
http://www.pcavionics.com/custserv/index.jsp
http://www.navzilla.com/ (min features low cost)
Many of the PDA based software GPS setups can accept real time weather and receive the data thru sat radio (XM radio) or a sat cel phone. Also they can be updated cheaper than Garmin (as they claim).
If you are on a budget, and you are NOT going IFR or EFIS there is no choice but handheld. If you want an EFIS I would consider the products that combine GPS map with EFIS. This is a good option, but if you are day VFR do you need EFIS. If you are going IFR you can could install a VOR/LOC/GPS/MB receiver (full IFR:
http://valavionics.com/p_ins422.html ) and use a (VFR) handheld GPS for situational awareness. However if you want to IFR GPS for enroute and approaches you must have a panel mount. You have no choice and you have to pay the price of admission to play that game. Some people don't blink an eye at a $30,000 panel. To each his own (bank account).
Cheers George